I work at a small ecommerce site and we're looking to move to all Amazon hosted services and I'm unsure the exact difference in RDS and SimpleDB. RDS can use MySQL, can SimpleDB not?
Simply put, I would assume that because your business model is e-commerce that you need transactional consistency in your data solution. Because of this, you should choose one of the RDS options (these are MySQL, Oracle or SQL Server).
AWS SimpleDB is a non-relational data store (or NoSQL), so what you get is flexibility (i.e. schema-less or schema-light) and scalability, but what you don't get is immediate (transactional) consistency and also the query pattern will not use joins.